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- PDB-2vrw: Critical structural role for the PH and C1 domains of the Vav1 ex... -

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Entry
Database: PDB / ID: 2vrw
TitleCritical structural role for the PH and C1 domains of the Vav1 exchange factor
Components
  • PROTO-ONCOGENE VAV
  • RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
KeywordsSIGNALING PROTEIN / LIPOPROTEIN / GTP-BINDING / METAL-BINDING / PROTO-ONCOGENE / PHOSPHOPROTEIN / EXCHANGE FACTOR / RAC / VAV / GTPASE / MEMBRANE / SH2 DOMAIN / SH3 DOMAIN / METHYLATION / ZINC-FINGER / PRENYLATION / GUANINE-NUCLEOTIDE RELEASING FACTOR / PHORBOL-ESTER BINDING / ADP-RIBOSYLATION / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


Azathioprine ADME / RAC2 GTPase cycle / CD28 dependent Vav1 pathway / Erythropoietin activates RAS / GPVI-mediated activation cascade / RHOA GTPase cycle / RHOG GTPase cycle / NRAGE signals death through JNK / RAC1 GTPase cycle / Signaling by SCF-KIT ...Azathioprine ADME / RAC2 GTPase cycle / CD28 dependent Vav1 pathway / Erythropoietin activates RAS / GPVI-mediated activation cascade / RHOA GTPase cycle / RHOG GTPase cycle / NRAGE signals death through JNK / RAC1 GTPase cycle / Signaling by SCF-KIT / VEGFR2 mediated vascular permeability / phosphorylation-dependent protein binding / G alpha (12/13) signalling events / regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / PIP3 activates AKT signaling / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / engulfment of apoptotic cell / ruffle assembly / NTRK2 activates RAC1 / Regulation of signaling by CBL / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / FCERI mediated MAPK activation / positive regulation of natural killer cell mediated cytotoxicity / respiratory burst / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Interleukin-3, Interleukin-5 and GM-CSF signaling / FCERI mediated Ca+2 mobilization / PCP/CE pathway / RHO GTPases activate CIT / cell projection assembly / RHO GTPases activate KTN1 / ruffle organization / Regulation of actin dynamics for phagocytic cup formation / cortical cytoskeleton organization / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / hepatocyte growth factor receptor signaling pathway / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / negative regulation of fibroblast migration / thioesterase binding / Azathioprine ADME / regulation of stress fiber assembly / Wnt signaling pathway, planar cell polarity pathway / sphingosine-1-phosphate receptor signaling pathway / motor neuron axon guidance / regulation of lamellipodium assembly / VEGFA-VEGFR2 Pathway / Nef and signal transduction / Sema4D mediated inhibition of cell attachment and migration / positive regulation of Rho protein signal transduction / Activation of RAC1 / positive regulation of cell-substrate adhesion / Ephrin signaling / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / CD28 dependent Vav1 pathway / lamellipodium assembly / Activation of RAC1 downstream of NMDARs / semaphorin-plexin signaling pathway / NRAGE signals death through JNK / regulation of cell size / Rac protein signal transduction / DSCAM interactions / small GTPase mediated signal transduction / establishment or maintenance of cell polarity / RHO GTPases activate PAKs / Rho GDP-dissociation inhibitor binding / ficolin-1-rich granule membrane / positive regulation of focal adhesion assembly / T cell differentiation / Sema3A PAK dependent Axon repulsion / RHO GTPases activate IQGAPs / EPH-ephrin mediated repulsion of cells / anatomical structure morphogenesis / positive regulation of cell adhesion / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / RHO GTPases Activate WASPs and WAVEs / RHO GTPases Activate NADPH Oxidases / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / phagocytosis / regulation of GTPase activity / regulation of actin cytoskeleton organization / positive regulation of lamellipodium assembly / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / positive regulation of substrate adhesion-dependent cell spreading / T cell activation / G protein activity / reactive oxygen species metabolic process / regulation of cell migration
Similarity search - Function
VAV1, SH2 domain / VAV1 protein, first SH3 domain / VAV1 protein, second SH3 domain / Protein vav1 / Vav, PH domain / Smooth muscle protein/calponin / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Dbl homology (DH) domain ...VAV1, SH2 domain / VAV1 protein, first SH3 domain / VAV1 protein, second SH3 domain / Protein vav1 / Vav, PH domain / Smooth muscle protein/calponin / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Dbl homology (DH) domain / Dbl Homology Domain; Chain A / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / small GTPase Rho family profile. / Small GTPase Rho / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Phorbol esters/diacylglycerol binding domain (C1 domain) / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain superfamily / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Calponin homology domain / Zinc finger phorbol-ester/DAG-type signature. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / CH domain superfamily / Calponin homology domain / Calponin homology (CH) domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Pleckstrin homology domain. / Pleckstrin homology domain / Small GTPase / Ras family / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Proto-oncogene vav / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRapley, J. / Tybulewicz, V. / Rittinger, K.
CitationJournal: Embo Rep. / Year: 2008
Title: Crucial Structural Role for the Ph and C1 Domains of the Vav1 Exchange Factor.
Authors: Rapley, J. / Tybulewicz, V. / Rittinger, K.
History
DepositionApr 16, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
B: PROTO-ONCOGENE VAV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0934
Polymers67,9622
Non-polymers1312
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-15.7 kcal/mol
Surface area32450 Å2
MethodPQS
Unit cell
Length a, b, c (Å)122.763, 62.143, 103.281
Angle α, β, γ (deg.)90.00, 118.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 / P21-RAC1 / RAS- LIKE PROTEIN TC25 / CELL MIGRATION-INDUCING GENE 5 PROTEIN / RAC1


Mass: 20462.746 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P63000
#2: Protein PROTO-ONCOGENE VAV / P95VAV / VAV1


Mass: 47499.234 Da / Num. of mol.: 1 / Fragment: RESIDUES 170-575
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET24B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P27870
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 50.91 % / Description: NONE
Crystal growpH: 9 / Details: 100MM BICINE PH9.0 10% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.117
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.117 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 57653 / % possible obs: 99.2 % / Observed criterion σ(I): 5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.2
Reflection shellResolution: 1.85→1.93 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.8 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→15 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.338 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2937 5.1 %RANDOM
Rwork0.203 ---
obs0.205 54863 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.36 Å2
2---0.58 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4400 0 2 471 4873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224498
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0311.9676069
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2425545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94323.917217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54615835
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6141534
X-RAY DIFFRACTIONr_chiral_restr0.0740.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023377
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.22151
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.23089
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2420
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5421.52821
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.90124400
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.46331901
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3284.51668
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.283 202
Rwork0.259 3906
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.9408-0.77140.77951.3813-0.10471.1312-0.1580.15190.1391-0.05340.03930.0722-0.11390.04030.1187-0.0301-0.0295-0.0283-0.03570.0407-0.0252-8.514-28.59216.8848
20.52880.60080.44491.22270.29230.58680.02010.0040.01210.04280.01580.03220.0312-0.0406-0.0358-0.019-0.00620.0126-0.03110.0042-0.0337-1.0518-43.234134.7584
31.1124-0.1691-0.47190.61040.19153.19940.02510.1084-0.0379-0.053-0.04390.05880.23260.18550.0188-0.01070.01250.0067-0.0356-0.0405-0.054922.7588-57.45881.9478
43.90541.0536-0.50632.17450.74881.5486-0.07920.0040.01340.0070.0644-0.05330.01370.04380.0148-0.06510.0006-0.0076-0.0341-0.0089-0.0228.3111-45.878424.8559
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 177
2X-RAY DIFFRACTION2B190 - 373
3X-RAY DIFFRACTION3B374 - 508
4X-RAY DIFFRACTION4B509 - 564

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